Comparative chloroplast genomics, phylogenetic relationships and molecular markers development of Aglaonema commutatum and seven green cultivars of Aglaonema

Aglaonema commutatum is a famous species in the Aglaonema genus, which has important ornamental and economic value. However, its chloroplast genome information and phylogenetic relationships among popular green cultivars of Aglaonema in southern China have not been reported. Herein, chloroplast genomes of one variety of A. commutatum and seven green cultivars of Aglaonema, namely, A. commutatum ‘San Remo’, ‘Kai Sa’, ‘Pattaya Beauty’, ‘Sapphire’, ‘Silver Queen’, ‘Snow White’, ‘White Gem’, and ‘White Horse Prince’, were sequenced and assembled for comparative analysis and phylogeny. These eight genomes possessed a typical quadripartite structure that consisted of a LSC region (90,799–91,486 bp), an SSC region (20,508–21,137 bp) and a pair of IR regions (26,661–26,750 bp). Each genome contained 112 different genes, comprising 79 protein-coding genes, 29 tRNA genes and 4 rRNA genes. The gene orders, GC contents, codon usage frequency, and IR/SC boundaries were highly conserved among these eight genomes. Long repeats, SSRs, SNPs and indels were analyzed among these eight genomes. Comparative analysis of 15 Aglaonema chloroplast genomes identified 7 highly variable regions, including trnH-GUG-exon1-psbA, trnS-GCU-trnG-UCC-exon1, trnY-GUA-trnE-UUC, psbC-trnS-UGA, trnF-GAA-ndhJ, ccsA-ndhD, and rps15-ycf1-D2. Reconstruction of the phylogenetic trees based on chloroplast genomes, strongly supported that Aglaonema was a sister to Anchomanes, and that the Aglaonema genus was classified into two sister clades including clade I and clade II, which corresponded to two sections, Aglaonema and Chamaecaulon, respectively. One variety and five cultivars, including A. commutatum ‘San Remo’, ‘Kai Sa’, ‘Pattaya Beauty’, ‘Silver Queen’, ‘Snow White’, and ‘White Horse Prince’, were classified into clade I; and the rest of the two cultivars, including ‘Sapphire’ and ‘White Gem’, were classified into clade II. Positive selection was observed in 34 protein-coding genes at the level of the amino acid sites among 77 chloroplast genomes of the Araceae family. Based on the highly variable regions and SSRs, 4 DNA markers were developed to differentiate the clade I and clade II in Aglaonema. In conclusion, this study provided chloroplast genomic resources for Aglaonema, which were useful for its classification and phylogeny.


Codon usage analysis
The codon usage of the 8 sequenced Aglaonema chloroplast genomes is shown in Table S3.Protein-coding genes contained 26,259 codons to 26,353 codons among these 8 genomes (Table S3).Among these codons, those for leucine and isoleucine were the first and second most common in these 8 genomes (Fig. 3, Table S3).The use of the codons ATG and TGG, encoding Met and Trp respectively, exhibited no bias (RSCU = 1.00) in these 8 Aglaonema chloroplast genomes (Fig. 3, Table S3).The codons with the three highest RSCU values (AGA, GCT, and TTA) and the four lowest RSCU values (AGC, GGC, CGC, and CTG) were found in the protein-coding genes codons of these 8 genomes (Table S3).Additionally, 29 codons with RSCU higher than 1.00 were A/T-ending codons and only one codon with RSCU higher than 1.00 was G/C-ending (Table S3).The results of RSCU > 1.00 indicated that these 8 Aglaonema genomes had a higher usage frequency for A/T-ending than G/C-ending.

Analyses of long repeats and SSRs
Long repeats of the 8 newly sequenced genomes were analyzed by REPuter and the results are displayed in Fig. 4 and Table S4.Among these 8 genomes, 'Pattaya Beauty' had the largest number (266), and 'Sapphire' had the smallest number (148) of long repeats (Fig. 4, Table S4).Four different types of long repeats were found, including forward, palindromic, reverse, and complement repeats.The number of forward repeats varied from 33 to 69, the number of palindromic repeats varied from 42 to 79, the number of reverse repeats varied from 41 to 80, and the number of complement repeats varied from 21 to 38 (Fig. 4A, Table S4).The length of long repeats varied among these 8 genomes (Fig. 4B, Table S4).Long repeats with lengths of 30-34 bp were found to be the most common in these 8 genomes, followed by 35-39 bp (Fig. 4B, Table S4).SSRs in the 8 newly sequenced genomes were also analyzed.The number of SSRs ranged from 110 to 123 (Fig. 5A, Table S5).Mononucleotide SSRs were the most abundant with numbers ranging from 52 to 58, followed by dinucleotide SSRs ranging from 23 to 28, tetranucleotide SSRs ranging from 16 to 21, trinucleotide SSRs ranging from 6 to 12, pentanucleotide SSRs ranging from 5 to 10, and hexanucleotide SSRs ranging from 0 to 2 (Fig. 5A, Table S5).It is interesting to find that hexanucleotide SSRs were not found in three cultivars, namely, 'Kai Sa' , 'Sapphire' and 'White Gem' (Fig. 5A, Table S5).SSRs were more frequently located in the LSC regions (80-91 loci) than in the SSC regions (14-27 loci) and IR regions (4-6 loci) of these 8 genomes (Fig. 5B, Table S5).Additionally, among these 8 genomes, most of the mononucleotide SSRs were A/T repeats, with numbers ranging from 52 to 58 (Fig. 5C, Table S5).In the dinucleotide repeats, the AT/AT repeats were observed most frequently, with numbers ranging from 21 to 27 (Fig. 5C, Table S5).In the trinucleotide repeats, the AAT/ ATT repeats were the richest type, with numbers ranging from 4 to 8 (Fig. 5C, Table S5).In the tetranucleotide category, the AAAT/ATTT repeats were the most abundant type, with numbers ranging from 7 to 12, followed by AATC/ATTG with numbers ranging from 5 to 6 (Fig. 5C, Table S5).

Comparative chloroplast genomics in the Aglaonema genus
Using the complete chloroplast genome of A. commutatum 'San Remo' as the reference, a comparative analysis based on mVISTA program was performed among 15 complete chloroplast genomes of Aglaonema, which included the 8 newly sequenced ones and 7 published ones from NCBI (Fig. 6).The results indicated that the LSC and SSC regions were more divergent than the two IR regions (Fig. 6).In the protein-coding regions, most protein-coding genes were highly conserved except for rps16, trnS, trnE, rpl32, trnV and ycf1 (Fig. 6).The highly divergent regions among these 15 genomes mainly located in the intergenic regions, including trnH-psbA, trnS-trnG, trnY-trnE and trnF-ndhJ in LSC region as well as ndhF-rpl32, ccsA-ndhD, and rps15-ycf1 in SSC region (Fig. 6).The CGview result also revealed that the IR regions were less divergent than the LSC and SSC regions (innermost 4th colour ring to outwards 18th ring in Fig. 2).In comparison to the chloroplast genome of A. commutatum 'San Remo' (innermost 4th colour ring in Fig. 2), the rest of the 14 chloroplast genomes showed four divergent regions in LSC (trnS-trnG, trnY-trnE, psbC-trnS, and trnF-ndhJ), two divergent regions in SSC (ccsA-ndhD and rps15-ycf1) and one divergent region in IRa (rpl22-rps19).

Molecular markers development based on the Aglaonema chloroplast genomes
To identify A. commutatum 'San Remo' and the seven green cultivars of Aglaonema, we selected several highly divergent regions and SSRs containing regions to develop the DNA markers.Finally, four markers could successfully discriminate some Aglaonema species and cultivars.In the present study, we only showed the results of the  S11, Fig. 7).Additionally, there were two other valid markers, namely, Primer1 and Primer3, which contained SSRs and were located in the psbA and trnK-UUU-exon1-rps16-exon2, respectively (Table S11).These four markers were used to differentiate 'Sapphire' and 'White Gem' from A. commutatum 'San Remo' , 'Kai Sa' , 'Pattaya Beauty' , 'Silver Queen' , 'Snow White' , and 'White Horse Prince' (Fig. 9, Fig. S4).Based on the results of the two phylogenetic trees, A. commutatum  S3).The results of these four DNA markers were consistent with the results of the phylogenetic trees, which could be used for further studies on identification of Aglaonema species and cultivars.

Discussion
In this study, 8 complete chloroplast genomes from Aglaonema in the Araceae family, were sequenced, assembled and performed for their comparative genomics with other related Aglaonema species and cultivars 8,13 .All these 8 genomes possessed a typical quadripartite structure, as reported for other Araceae species, such as A. modestum 8 , Epipremnum aureum 11 , A. costatum 13 , Anthurium huixtlense and Pothos scandens 16 .These 8 genomes each encoded 112 different genes, including 79 protein-coding genes, 4 rRNA genes, and 29 tRNA genes (Table 1).This result was consistent with the protein-coding gene number, rRNA gene number and tRNA gene number in a previous report for A. modestum, 'Red Valentine' , 'Hong Yan' , and 'Hong Jian' 8 .However, there were some variations in these 8 chloroplast genome lengths, with A. commutatum 'San Remo' having the longest genome length, which was 166,123 bp, and 'Silver Queen' being the shortest, at only 164,789 bp (Table 1).Notably, the chloroplast genomes lengths varied by 1.3 kb herein.This finding was also reported for the Polystachya species with about 3.8 kb differences in chloroplast genome lengths 19 .The reasons for genome length variations may be because of the number of genes or introns loss and gain, IR contraction and expansion, and variations of the intergenic regions 13,17,19,24 .In many chloroplast genomes of higher plants, leucine and cysteine were identified as the most common and the least common codons, respectively 8,17,19,20,25 , and most codons bias showed higher A/T-ending than G/C-ending 8,17,19,20,25 .Compared to the result of this study, it was confirmed that the 8 chloroplast genomes of Aglaonema exhibited the same characteristics as those of reported higher plants 8,17,19,20,25 .
Many studies proved that highly divergent sequences, SSRs and long repeats of chloroplast genome sequences were useful for studies on phylogenetic relationships, species/cultivar identification and molecular markers development 18,[26][27][28] .Research has shown that Colocasia gigantea, Caladium bicolor, and Xanthosoma sagittifolium could be successfully identified with strong support using chloroplast genome sequences, and three www.nature.com/scientificreports/DNA barcodes (atpH-atpI + psaC-ndhE, atpH-atpI + trnS-trnG, atpH-atpI + psaC-ndhE + trnS-trnG) harboured highly variable regions to distinguish species in the Aroideae subfamily 18 .In the three varieties of Scutellaria baicalensis, chloroplast genome can be used as a super-barcode for identification 26 .In Gleditsia sinensis and G. japonica, the mini-barcode of primers ZJ818F-1038R (ycf1b) was proven to precisely discriminate between these two species 27 .In the Dianthus species, one valid DNA marker in the clpP-psbB region, was used to differentiate D. caryophyllus, D. barbatus, and two cultivars from D. superbus, D. chinensis, and one hybrid offspring F1 28 .In this study, seven highly variable regions were detected among 15 chloroplast genomes of Aglaonema, including trnH-GUG-exon1-psbA, trnS-GCU-trnG-UCC-exon1, trnY-GUA-trnE-UUC , psbC-trnS-UGA , trnF-GAA-ndhJ, ccsA-ndhD, and rps15-ycf1-D2 (Fig. 7).Besides the highly variable regions, SSRs and long repeats were also retrieved (Figs. 4 and 5).Among these 8 genomes, SSRs were more frequently located in the LSC regions than in the SSC regions and IR regions (Fig. 5).These findings were in agreement with results from a previous study reported in A. modestum 8 .Based on these results, several regions where sequences with high divergence and/or SSR loci were used to develop DNA markers.After PCR and sequencing, we found that 4 DNA markers could be used to differentiate 'Sapphire' and 'White Gem' from A. commutatum 'San Remo' , 'Kai Sa' , 'Pattaya Beauty' , 'Silver Queen' , 'Snow White' , and 'White Horse Prince' (Fig. 9, Fig. S4).Therefore, these highly variable regions and SSRs could serve to enrich the molecular marker resources of Aglaonema for studying its phylogeny and identification.
In this study, SNPs and indels were also identified among these 8 newly sequenced genomes (Table 3, Tables S6  and S7).It is worth noting that 1 SNP and 1 insertion exist between 'Sapphire' and 'White Gem' (Table 3).The SNP was located in psaC, and the insertion was found in rps12 (Tables S6 and S7).As we know, 'White Gem' was a bud mutation among a population of tissue-cultured 'Sapphire' plants (Fig. 1).Therefore, psaC and rps12 genes could be used to differentiate these two cultivars at the molecular level.By comparison, 'Red Valentine' versus 'Hong Jian' and 'Red Valentine' versus 'Hong Yan' had no SNPs/indels in a previous study, in which 'Hong Jian' and 'Hong Yan' were two bud mutations found among tissue-cultured 'Red Valentine' plants 8 .These comparisons indicated that the chloroplast genomes may undergo variation between the tissue-cultured mutation of 'White Gem' and 'Sapphire' .Additionally, the other 12 comparison pairs, also contained many SNPs and indels (Table 3, Tables S6 and S7).These SNPs and indels could be used to identify A. commutatum 'San Remo' and seven green cultivars of Aglaonema.
Based on chloroplast genomes, our phylogenetic results strongly supported that the 15 individuals of Aglaonema species and cultivars can be classified into two clades, namely, clade I and clade II (Fig. 8, Fig.S3).In a previous study, based on morphological characteristics, the Aglaonema genus was classified into two sections, namely, Aglaonema and Chamaecaulon 1 .By comparison, the clade I and clade II in our phylogenetic trees corresponded to the two sections using morphological classification, namely, Aglaonema and Chamaecaulon, respectively.Therefore, our phylogenetic results support the morphological classification of the Aglaonema genus 1 .In a previous report, the phylogenetic tree based on whole chloroplast genomes strongly supported monophyletic of the Aglaonema genus 8 .The reasons may be because this report did not sample plenty of Aglaonema species and cultivars.In another study with 54 Aglaonema species and cultivars, they were divided into seven clusters by 314 polymorphic amplified fragment length polymorphism (AFLP) markers 2 .This may be because the small cluster in the main cluster was also as a cluster in that study 2 .In fact, from the dendrogram of the 54 Aglaonema species and cultivars, there were two main clusters 2 .Regarding the Araceae family, phylogenetic relationships among the 7 subfamilies of Aroideae, Lasioideae, Lemnoideae, Monsteroideae, Orontioideae, Pothoideae, and Zamioculcadoideae, were strongly supported (Fig. 8, Fig.S3).Our phylogenetic trees reconstructed by complete chloroplast genomes for the Araceae family were in agreement with previous studies 8,10,13,14 .In conclusion, there are sufficient complete chloroplast genomes with good reliability to understand the phylogenetic relationships of the Aglaonema genus and Araceae family.
In the current study, 34 protein-coding genes with positive selection sites among 77 complete chloroplast genomes of the Araceae family were identified (Tables S9 and S10).Current comparative studies have revealed that our findings revealed more genes under positive selection than the results from the 16 chloroplast genomes of Araceae 8 and 17 chloroplast genomes of Aroideae 18 , but less genes under positive selection than the results from the 14 chloroplast genomes of Araceae 12 .These differences may be because these three studies used different chloroplast genomes of the Araceae family.These comparisons also reflected the complexity of chloroplast genome evolution in the Araceae family.In the present study, among 34 protein-coding genes with positive selection sites, ycf2 harboured the highest number of positive amino acids sites (72) (Table S10), suggesting that ycf2 may play an important role in the adaptive evolution of the Araceae family.Meanwhile, rpoC2, rbcL, matK, atpA, atpB, rpoB and ndhF also possessed relatively high positive selection sites (23, 12, 7, 6, 5, 5 and 4,  respectively).Recent studies have showed that some of these 34 protein-coding genes under positive selection may be very common in higher plants 13,17,20,23,[29][30][31] .For examples, rbcL, rps8 and ycf2 have been identified under positive selection in the Monsteroideae subfamily 13 ; ccsA, ndhA, ndhB, rbcL, rpoC1, rpoC2, rps18, ycf2 and ycf4 have been identified under positive selection in the Zingiberoideae subfamily 17 ; ccsA, ndhA, ndhB, psbA, psbB, psbC, rbcL, rpoC2, rps7, atpA, atpB, rpoA, rps3, clpP, ycf2 and ycf3 have been identified under positive selection in the Zingiber genus 20,29 ; psbA, psbB, atpA, atpB, atpF, atpI, ndhA, ndhB, ndhC, ndhF, rps3, rps7, rps8, rps15, rpoB, rpoC1, rpoC2, rbcL, clpP, matK, ycf3 and ycf4 have been identified under positive selection in the Zingiberales order 23 ; rpoC1, rpoC2, rps15, ccsA, rbcL, ycf2 and ycf4 have been reported as positive selection in orchid 30 ; and rpoC2, atpF, atpI, and rpl14 have been identified under positive selection in Allium 31 .For the one hand, the Araceae species had diverse plant morphologies, such as the perennial herbaceous plants, and epiphytic, climbing shrubs or subshrubs; for example, A. modestum was a perennial herb with stem erect, while Pothos cathcartii was a climbing subshrub with a length of more than 5 m 3,4 .For the other hand, the Araceae species had different natural habitats; for instance, A. modestum lived in dense forests at altitudes of 500-1700 m, whereas P. cathcartii was epiphytic on the trunk of dense forests at altitudes of 500-1600 m 3,4

Plant materials, chloroplast DNA extraction, and sequencing
Fresh leaves of one species and seven green cultivars of Aglaonema, including A. commutatum 'San Remo', 'Kai Sa' , 'Pattaya Beauty' , 'Sapphire' , 'Silver Queen' , 'Snow White' , 'White Gem' , and 'White Horse Prince' (Fig. 1), were collected from the resource garden (23°23′ N, 113°26′ E) of the environmental horticulture research institute at the Guangdong Academy of Agricultural Sciences, Guangzhou, China. A. commutatum 'San Remo' had solid dark green petioles and dark green leaves with medium grey green blotches (Fig. 1A).'Kai Sa' had dark green petioles and blotches and marginal zone green leaves (Fig. 1B).'Pattaya Beauty' had green petioles and leaves with marginal zones dark green and along midribs large grey green blotches (Fig. 1C).'Sapphire' had light red petioles and dark green leaves with midribs and margins red (Fig. 1D).'Silver Queen' had dark green petioles and blotches grey green leaves (Fig. 1E).'Snow White' had white petioles and stripes grey green leaves (Fig. 1F).'White Gem' , bud mutation found among a population of tissue-cultured 'Sapphire' plants, had white petioles and dark green leaves with midribs and margins white (Fig. 1G).'White Horse Prince' had white petioles and strong yellow-green leaves along midribs and at margins white (Fig. 1H).Each sample was quickly frozen in liquid nitrogen and then stored at − 80 °C until use.Chloroplast genomic DNA was extracted using the modified sucrose gradient centrifugation method 32 .DNA quality and concentration were examined by using 1% (w/v) agarose gel electrophoresis and NanoDrop 2000 microspectrometer (Wilmington, DE, USA).Each qualified DNA was used for construction of a DNA library with fragments of about 350 bp, and then sequenced on an Illumina NovaSeq 6000 platform with 150 bp paired-end reads length (Biozeron, Shanghai, China).The original raw data were checked using FastQC v. 0.11.9 (http:// www.bioin forma tics.babra ham.ac.uk/ proje cts/ fastqc/), and then filtered by Trimmomatic v. 0.39 33 with default settings to delete adaptors and low-quality reads.

Analyses of codon usage, long repeats and SSRs
The codon usage of the 8 chloroplast genomes of Aglaonema was detected using MEGA v. 7.0 42 with default settings.Amino acid frequency was also calculated by the percentage of the codons encoding the same amino acid divided by the total number of codons.Simple sequence repeats (SSRs) were identified using the online MISA-web 43 .SSRs were detected with the thresholds of 10 repeat units for mononucleotides, 5 repeat units for dinucleotides, 4 repeat units for trinucleotides, and 3 repeat units for tetra-, penta-and hexanucleotides.Long repeats including forward, palindrome, reverse and complement repeats, were analyzed using REPuter 44 with repeat sizes ≧ 30 bp and sequences identity ≧ 90%.

Comparative genomics analysis in the Aglaonema genus
The newly sequenced 8 chloroplast genomes of Aglaonema for LSC/IR and SSC/IR boundaries and their adjacent genes were analyzed using IRscope 45 .First, to analyze the differences among the chloroplast genomes of A. commutatum 'San Remo' and 7 green cultivars of Aglaonema, the newly sequenced 8 chloroplast genomes of

Figure 2 .
Figure 2. Chloroplast genome map of A. commutatum 'San Remo' (the outermost three rings) and CGView comparison of 15 Aglaonema chloroplast genomes (the inter rings with different colours).Genes belonging to different functional groups are shown in different colours in the outermost first ring.Genes shown on the outside of the outermost first ring are transcribed counter-clockwise and on the inside clockwise.Gray arrowheads indicate the direction of the genes.The tRNA genes are indicated by a one-letter code of amino acids with anticodons.LSC, large single-copy region; SSC, small single-copy region; and IR, inverted repeat.The innermost first black ring indicates the chloroplast genome size of A. commutatum 'San Remo' .The innermost second and third rings indicate GC content and GC skew deviations in the chloroplast genome of A. commutatum 'San Remo' , respectively: GC skew + indicates G > C, and GC skew-indicates G < C. From the innermost fourth color ring to the outwards 18th ring in turn: A. commutatum 'San Remo' , A. costatum, A. modestum, Aglaonema 'Hong Yan' , Aglaonema 'Hong Jian' , Aglaonema 'Kai Sa' , Aglaonema 'Lady Valentine' , Aglaonema 'Pattaya Beauty' , Aglaonema 'Red Valentine' , Aglaonema 'Red Vein' , Aglaonema 'Sapphire' , Aglaonema 'Silver Queen' , Aglaonema 'Snow White' , Aglaonema 'White Gem' , and Aglaonema 'White Horse Prince'; chloroplast genome similar and highly divergent locations are represented by continuous and interrupted track lines, respectively.The 8 newly sequenced Aglaonema chloroplast genomes in this study are in bold.

Figure 3 .
Figure 3. Codon content of 20 amino acids of all protein-coding genes in the 8 newly sequenced Aglaonema chloroplast genomes.

Figure 4 .
Figure 4. Long repeat sequences distribution in the 8 newly sequenced Aglaonema chloroplast genomes.(A) Total number of four long repeat types.(B) Length distribution of long repeats in each sequenced chloroplast genome.

Figure 5 .
Figure 5. Distribution of SSRs in the 8 newly sequenced Aglaonema chloroplast genomes.(A) Number of different SSR types.(B) Frequency of the identified SSRs in the LSC, SSC and IR regions.(C) Frequency of the identified SSRs in different repeat class types.

Figure 6 .
Figure 6.Chloroplast genome comparison of 15 Aglaonema chloroplast genomes using A. commutatum 'San Remo' as the reference.Gray arrows and thick black lines above the alignment indicate gene orientation.Purple bars represent exons, sky-blue bars represent untranslated regions (UTRs), red bars represent non-coding sequences (CNS), gray bars represent mRNA and white regions represent sequence differences among analyzed chloroplast genomes.The y-axis represents the identity percentage ranging from 50 to 100%.The 8 newly sequenced Aglaonema chloroplast genomes in this study are in bold.

Figure 7 .
Figure 7. Comparisons of nucleotide diversity (Pi) values among 15 complete chloroplast genomes of the genus Aglaonema.(A) Protein-coding genes.Protein-coding genes with Pi values > 0.009 are labelled with gene names.(B) Intergenic regions.Intergenic regions with Pi values > 0.022 are labelled with intergenic region names.

Figure 8 .
Figure 8. Phylogenetic tree of 77 complete chloroplast genomes of the Araceae family using the ML method.The 8 newly sequenced Aglaonema chloroplast genomes in this study are in bold.

Table 1 .
Characteristics of the eight newly sequenced chloroplast genomes of Aglaonema.GC, guaninecytosine; PCD, protein-coding genes; LSC, large single copy region; SSC, small single copy region; and IR, inverted repeat.

Table 3 .
SNPs and indels among the eight newly sequenced chloroplast genomes of Aglaonema.
Vol.:(0123456789) Scientific Reports | (2024) 14:11820 | https://doi.org/10.1038/s41598-024-62586-ywww.nature.com/scientificreports/ involved in photosystem, ATP synthase, NADH dehydrogenase and ribosome, may play important roles during the evolution and adaptation of Araceae plants to their natural habitats.In this study, 8 complete chloroplast genomes from A. commutatum 'San Remo', 'Kai Sa' , 'Pattaya Beauty' , 'Sapphire' , 'Silver Queen' , 'Snow White' , 'White Gem' and 'White Horse Prince' , were sequenced, assembled and reported for the first time.These 8 genomes displayed a typical quadripartite structure and each genome contained 112 different genes, including 79 protein-coding genes, 29 tRNA genes and 4 rRNA genes, with genome lengths of 164,789-166,123 bp.The gene orders, GC contents, codon usage frequency, and IR/SC boundaries showed high degree of conservation.Comparative analyses of 15 complete chloroplast genomes of Aglaonema identified 7 highly variable regions, which can be used as potential markers for phylogeny and species identification.Both ML and BI phylogenetic trees based on chloroplast genomes strongly supported that the Aglaonema genus was classified into two clades, namely, clade I and clade II.These two clades corresponded to two sections, Aglaonema and Chamaecaulon, respectively.Based on the highly variable regions and SSRs, 4 DNA markers were developed to differentiate the two clades in Aglaonema.Finally, 34 protein-coding genes were under positive selection at levels of amino acids with high posterior probabilities among 77 complete chloroplast genomes of the Araceae family.These results enrich the genomic resources of the Aglaonema genus and Araceae family, which are useful for classification of Aglaonema and chloroplast genome evolution of Araceae.